@article{17968, abstract = {While the electrical conductivity of bulk-scale group 14 materials such as diamond carbon, silicon, and germanium is well understood, there is a gap in knowledge regarding the conductivity of these materials at the nano and molecular scales. Filling this gap is important because integrated circuits have shrunk so far that their active regions, which rely so heavily on silicon and germanium, begin to resemble ornate molecules rather than extended solids. Here we unveil a new approach for synthesizing atomically discrete wires of germanium and present the first conductance measurements of molecular germanium using a scanning tunneling microscope-based break-junction (STM-BJ) technique. Our findings show that germanium and silicon wires are nearly identical in conductivity at the molecular scale, and that both are much more conductive than aliphatic carbon. We demonstrate that the strong donor ability of C–Ge σ-bonds can be used to raise the energy of the anchor lone pair and increase conductance. Furthermore, the oligogermane wires behave as conductance switches that function through stereoelectronic logic. These devices can be trained to operate with a higher switching factor by repeatedly compressing and elongating the molecular junction.}, author = {Su, Timothy A. and Li, Haixing and Zhang, Vivian and Neupane, Madhav and Batra, Arunabh and Klausen, Rebekka S. and Kumar, Bharat and Steigerwald, Michael L. and Venkataraman, Latha and Nuckolls, Colin}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, number = {38}, pages = {12400--12405}, publisher = {American Chemical Society}, title = {{Single-molecule conductance in atomically precise Germanium wires}}, doi = {10.1021/jacs.5b08155}, volume = {137}, year = {2015}, } @article{17969, abstract = {Recent experiments have shown that transport properties of molecular-scale devices can be reversibly altered by the surrounding solvent. Here, we use a combination of first-principles calculations and experiment to explain this change in transport properties through a shift in the local electrostatic potential at the junction caused by nearby conducting and solvent molecules chemically bound to the electrodes. This effect is found to alter the conductance of 4,4′-bipyridine-gold junctions by more than 50%. Moreover, we develop a general electrostatic model that quantitatively relates the conductance and dipoles associated with the bound solvent and conducting molecules. Our work shows that solvent-induced effects can be used to control charge and energy transport at molecular-scale interfaces.}, author = {Kotiuga, Michele and Darancet, Pierre and Arroyo, Carlos R. and Venkataraman, Latha and Neaton, Jeffrey B.}, issn = {1530-6992}, journal = {Nano Letters}, number = {7}, pages = {4498--4503}, publisher = {American Chemical Society}, title = {{Adsorption-induced solvent-based electrostatic gating of charge transport through molecular junctions}}, doi = {10.1021/acs.nanolett.5b00990}, volume = {15}, year = {2015}, } @article{17970, abstract = {Charge transport properties of metal–molecule interfaces depend strongly on the character of molecule–electrode interactions. Although through-bond coupled systems have attracted the most attention, through-space coupling is important in molecular systems when, for example, through-bond coupling is suppressed due to quantum interference effects. To date, a probe that clearly distinguishes these two types of coupling has not yet been demonstrated. Here, we investigate the origin of flicker noise in single molecule junctions and demonstrate how the character of the molecule–electrode coupling influences the flicker noise behavior of single molecule junctions. Importantly, we find that flicker noise shows a power law dependence on conductance in all junctions studied with an exponent that can distinguish through-space and through-bond coupling. Our results provide a new and powerful tool for probing and understanding coupling at the metal-molecule interface.}, author = {Adak, Olgun and Rosenthal, Ethan and Meisner, Jeffery and Andrade, Erick F. and Pasupathy, Abhay N. and Nuckolls, Colin and Hybertsen, Mark S. and Venkataraman, Latha}, issn = {1530-6992}, journal = {Nano Letters}, number = {6}, pages = {4143--4149}, publisher = {American Chemical Society}, title = {{Flicker noise as a probe of electronic interaction at metal–single molecule interfaces}}, doi = {10.1021/acs.nanolett.5b01270}, volume = {15}, year = {2015}, } @article{17971, abstract = {We study the impact of electrode band structure on transport through single-molecule junctions by measuring the conductance of pyridine-based molecules using Ag and Au electrodes. Our experiments are carried out using the scanning tunneling microscope based break-junction technique and are supported by density functional theory based calculations. We find from both experiments and calculations that the coupling of the dominant transport orbital to the metal is stronger for Au-based junctions when compared with Ag-based junctions. We attribute this difference to relativistic effects, which result in an enhanced density of d-states at the Fermi energy for Au compared with Ag. We further show that the alignment of the conducting orbital relative to the Fermi level does not follow the work function difference between two metals and is different for conjugated and saturated systems. We thus demonstrate that the details of the molecular level alignment and electronic coupling in metal–organic interfaces do not follow simple rules but are rather the consequence of subtle local interactions.}, author = {Adak, Olgun and Korytár, Richard and Joe, Andrew Y. and Evers, Ferdinand and Venkataraman, Latha}, issn = {1530-6992}, journal = {Nano Letters}, number = {6}, pages = {3716--3722}, publisher = {American Chemical Society}, title = {{Impact of electrode density of states on transport through pyridine-linked single molecule junctions}}, doi = {10.1021/acs.nanolett.5b01195}, volume = {15}, year = {2015}, } @article{17972, abstract = {Molecular electronics aims to miniaturize electronic devices by using subnanometre-scale active components1,2,3. A single-molecule diode, a circuit element that directs current flow4, was first proposed more than 40 years ago5 and consisted of an asymmetric molecule comprising a donor–bridge–acceptor architecture to mimic a semiconductor p–n junction. Several single-molecule diodes have since been realized in junctions featuring asymmetric molecular backbones6,7,8, molecule–electrode linkers9 or electrode materials10. Despite these advances, molecular diodes have had limited potential for applications due to their low conductance, low rectification ratios, extreme sensitivity to the junction structure and high operating voltages7,8,9,11,12. Here, we demonstrate a powerful approach to induce current rectification in symmetric single-molecule junctions using two electrodes of the same metal, but breaking symmetry by exposing considerably different electrode areas to an ionic solution. This allows us to control the junction's electrostatic environment in an asymmetric fashion by simply changing the bias polarity. With this method, we reliably and reproducibly achieve rectification ratios in excess of 200 at voltages as low as 370 mV using a symmetric oligomer of thiophene-1,1-dioxide13,14. By taking advantage of the changes in the junction environment induced by the presence of an ionic solution, this method provides a general route for tuning nonlinear nanoscale device phenomena, which could potentially be applied in systems beyond single-molecule junctions.}, author = {Capozzi, Brian and Xia, Jianlong and Adak, Olgun and Dell, Emma J. and Liu, Zhen-Fei and Taylor, Jeffrey C. and Neaton, Jeffrey B. and Campos, Luis M. and Venkataraman, Latha}, issn = {1748-3395}, journal = {Nature Nanotechnology}, number = {6}, pages = {522--527}, publisher = {Springer Nature}, title = {{Single-molecule diodes with high rectification ratios through environmental control}}, doi = {10.1038/nnano.2015.97}, volume = {10}, year = {2015}, } @article{17973, abstract = {Here we study the stability and rupture of molecular junctions under high voltage bias at the single molecule/single bond level using the scanning tunneling microscope-based break-junction technique. We synthesize carbon-, silicon-, and germanium-based molecular wires terminated by aurophilic linker groups and study how the molecular backbone and linker group affect the probability of voltage-induced junction rupture. First, we find that junctions formed with covalent S–Au bonds are robust under high voltage and their rupture does not demonstrate bias dependence within our bias range. In contrast, junctions formed through donor–acceptor bonds rupture more frequently, and their rupture probability demonstrates a strong bias dependence. Moreover, we find that the junction rupture probability increases significantly above ∼1 V in junctions formed from methylthiol-terminated disilanes and digermanes, indicating a voltage-induced rupture of individual Si–Si and Ge–Ge bonds. Finally, we compare the rupture probabilities of the thiol-terminated silane derivatives containing Si–Si, Si–C, and Si–O bonds and find that Si–C backbones have higher probabilities of sustaining the highest voltage. These results establish a new method for studying electric field breakdown phenomena at the single molecule level.}, author = {Li, Haixing and Su, Timothy A. and Zhang, Vivian and Steigerwald, Michael L. and Nuckolls, Colin and Venkataraman, Latha}, issn = {1520-5126}, journal = {Journal of the American Chemical Society}, number = {15}, pages = {5028--5033}, publisher = {American Chemical Society}, title = {{Electric field breakdown in single molecule junctions}}, doi = {10.1021/ja512523r}, volume = {137}, year = {2015}, } @article{17974, abstract = {Guest editors Dirk M. Guldi, Hiroshi Nishihara and Latha Venkataraman introduce the Molecular Wires issue of "Chemical Society Reviews".}, author = {Guldi, Dirk M. and Nishihara, Hiroshi and Venkataraman, Latha}, issn = {1460-4744}, journal = {Chemical Society Reviews}, number = {4}, pages = {842--844}, publisher = {Royal Society of Chemistry}, title = {{Molecular wires}}, doi = {10.1039/c5cs90010g}, volume = {44}, year = {2015}, } @article{17975, abstract = {A new intersection between reaction chemistry and electronic circuitry is emerging from the ultraminiaturization of electronic devices. Over decades chemists have developed a nuanced understanding of stereoelectronics to establish how the electronic properties of molecules relate to their conformation; the recent advent of single-molecule break-junction techniques provides the means to alter this conformation with a level of control previously unimagined. Here we unite these ideas by demonstrating the first single-molecule switch that operates through a stereoelectronic effect. We demonstrate this behaviour in permethyloligosilanes with methylthiomethyl electrode linkers. The strong σ conjugation in the oligosilane backbone couples the stereoelectronic properties of the sulfur–methylene σ bonds that terminate the molecule. Theoretical calculations support the existence of three distinct dihedral conformations that differ drastically in their electronic character. We can shift between these three species by simply lengthening or compressing the molecular junction, and, in doing so, we can switch conductance digitally between two states.}, author = {Su, Timothy A. and Li, Haixing and Steigerwald, Michael L. and Venkataraman, Latha and Nuckolls, Colin}, issn = {1755-4349}, journal = {Nature Chemistry}, number = {3}, pages = {215--220}, publisher = {Springer Nature}, title = {{Stereoelectronic switching in single-molecule junctions}}, doi = {10.1038/nchem.2180}, volume = {7}, year = {2015}, } @article{17976, abstract = {To develop advanced materials for electronic devices, it is of utmost importance to design organic building blocks with tunable functionality and to study their properties at the molecular level. For organic electronic and photovoltaic applications, the ability to vary the nature of charge carriers and so create either electron donors or acceptors is critical. Here we demonstrate that charge carriers in single-molecule junctions can be tuned within a family of molecules that contain electron-deficient thiophene-1,1-dioxide (TDO) building blocks. Oligomers of TDO were designed to increase electron affinity and maintain delocalized frontier orbitals while significantly decreasing the transport gap. Through thermopower measurements we show that the dominant charge carriers change from holes to electrons as the number of TDO units is increased. This results in a unique system in which the charge carrier depends on the backbone length, and provides a new means to tune p- and n-type transport in organic materials.}, author = {Dell, Emma J. and Capozzi, Brian and Xia, Jianlong and Venkataraman, Latha and Campos, Luis M.}, issn = {1755-4349}, journal = {Nature Chemistry}, number = {3}, pages = {209--214}, publisher = {Springer Nature}, title = {{Molecular length dictates the nature of charge carriers in single-molecule junctions of oxidized oligothiophenes}}, doi = {10.1038/nchem.2160}, volume = {7}, year = {2015}, } @article{1802, abstract = {Noncoding variants in the human MIR137 gene locus increase schizophrenia risk with genome-wide significance. However, the functional consequence of these risk alleles is unknown. Here we examined induced human neurons harboring the minor alleles of four disease-associated single nucleotide polymorphisms in MIR137. We observed increased MIR137 levels compared to those in major allele–carrying cells. microRNA-137 gain of function caused downregulation of the presynaptic target genes complexin-1 (Cplx1), Nsf and synaptotagmin-1 (Syt1), leading to impaired vesicle release. In vivo, miR-137 gain of function resulted in changes in synaptic vesicle pool distribution, impaired induction of mossy fiber long-term potentiation and deficits in hippocampus-dependent learning and memory. By sequestering endogenous miR-137, we were able to ameliorate the synaptic phenotypes. Moreover, reinstatement of Syt1 expression partially restored synaptic plasticity, demonstrating the importance of Syt1 as a miR-137 target. Our data provide new insight into the mechanism by which miR-137 dysregulation can impair synaptic plasticity in the hippocampus.}, author = {Siegert, Sandra and Seo, Jinsoo and Kwon, Ester and Rudenko, Andrii and Cho, Sukhee and Wang, Wenyuan and Flood, Zachary and Martorell, Anthony and Ericsson, Maria and Mungenast, Alison and Tsai, Lihuei}, issn = {1546-1726}, journal = {Nature Neuroscience}, pages = {1008 -- 1016}, publisher = {Springer Nature}, title = {{The schizophrenia risk gene product miR-137 alters presynaptic plasticity}}, doi = {10.1038/nn.4023}, volume = {18}, year = {2015}, } @article{1803, abstract = {Repeated stress has been suggested to underlie learning and memory deficits via the basolateral amygdala (BLA) and the hippocampus; however, the functional contribution of BLA inputs to the hippocampus and their molecular repercussions are not well understood. Here we show that repeated stress is accompanied by generation of the Cdk5 (cyclin-dependent kinase 5)-activator p25, up-regulation and phosphorylation of glucocorticoid receptors, increased HDAC2 expression, and reduced expression of memoryrelated genes in the hippocampus. A combination of optogenetic and pharmacosynthetic approaches shows that BLA activation is both necessary and sufficient for stress-associated molecular changes and memory impairments. Furthermore, we show that this effect relies on direct glutamatergic projections from the BLA to the dorsal hippocampus. Finally, we show that p25 generation is necessary for the stress-induced memory dysfunction. Taken together, our data provide a neural circuit model for stress-induced hippocampal memory deficits through BLA activity-dependent p25 generation.}, author = {Rei, Damien and Mason, Xenos and Seo, Jinsoo and Gräff, Johannes and Rudenko, Andrii and Wang, Jùn and Rueda, Richard and Sandra Siegert and Cho, Sukhee and Canter, Rebecca G and Mungenast, Alison E and Deisseroth, Karl A and Tsai, Lihuei}, journal = {PNAS}, number = {23}, pages = {7291 -- 7296}, publisher = {National Academy of Sciences}, title = {{Basolateral amygdala bidirectionally modulates stress induced hippocampal learning and memory deficits through a p25/Cdk5-dependent pathway}}, doi = {10.1073/pnas.1415845112}, volume = {112}, year = {2015}, } @article{1804, abstract = {It is known that in classical fluids turbulence typically occurs at high Reynolds numbers. But can turbulence occur at low Reynolds numbers? Here we investigate the transition to turbulence in the classic Taylor-Couette system in which the rotating fluids are manufactured ferrofluids with magnetized nanoparticles embedded in liquid carriers. We find that, in the presence of a magnetic field transverse to the symmetry axis of the system, turbulence can occur at Reynolds numbers that are at least one order of magnitude smaller than those in conventional fluids. This is established by extensive computational ferrohydrodynamics through a detailed investigation of transitions in the flow structure, and characterization of behaviors of physical quantities such as the energy, the wave number, and the angular momentum through the bifurcations. A finding is that, as the magnetic field is increased, onset of turbulence can be determined accurately and reliably. Our results imply that experimental investigation of turbulence may be feasible by using ferrofluids. Our study of transition to and evolution of turbulence in the Taylor-Couette ferrofluidic flow system provides insights into the challenging problem of turbulence control.}, author = {Altmeyer, Sebastian and Do, Younghae and Lai, Ying}, journal = {Scientific Reports}, publisher = {Nature Publishing Group}, title = {{Transition to turbulence in Taylor-Couette ferrofluidic flow}}, doi = {10.1038/srep10781}, volume = {5}, year = {2015}, } @article{1805, abstract = {We consider the problem of deciding whether the persistent homology group of a simplicial pair (K,L) can be realized as the homology H∗(X) of some complex X with L ⊂ X ⊂ K. We show that this problem is NP-complete even if K is embedded in double-struck R3. As a consequence, we show that it is NP-hard to simplify level and sublevel sets of scalar functions on double-struck S3 within a given tolerance constraint. This problem has relevance to the visualization of medical images by isosurfaces. We also show an implication to the theory of well groups of scalar functions: not every well group can be realized by some level set, and deciding whether a well group can be realized is NP-hard.}, author = {Attali, Dominique and Bauer, Ulrich and Devillers, Olivier and Glisse, Marc and Lieutier, André}, journal = {Computational Geometry: Theory and Applications}, number = {8}, pages = {606 -- 621}, publisher = {Elsevier}, title = {{Homological reconstruction and simplification in R3}}, doi = {10.1016/j.comgeo.2014.08.010}, volume = {48}, year = {2015}, } @article{1807, abstract = {We study a double Cahn-Hilliard type functional related to the Gross-Pitaevskii energy of two-components Bose-Einstein condensates. In the case of large but same order intercomponent and intracomponent coupling strengths, we prove Γ-convergence to a perimeter minimisation functional with an inhomogeneous surface tension. We study the asymptotic behavior of the surface tension as the ratio between the intercomponent and intracomponent coupling strengths becomes very small or very large and obtain good agreement with the physical literature. We obtain as a consequence, symmetry breaking of the minimisers for the harmonic potential.}, author = {Goldman, Michael and Royo-Letelier, Jimena}, journal = {ESAIM - Control, Optimisation and Calculus of Variations}, number = {3}, pages = {603 -- 624}, publisher = {EDP Sciences}, title = {{Sharp interface limit for two components Bose-Einstein condensates}}, doi = {10.1051/cocv/2014040}, volume = {21}, year = {2015}, } @article{1808, author = {Gupta, Ashutosh and Henzinger, Thomas A}, journal = {ACM Transactions on Modeling and Computer Simulation}, number = {2}, publisher = {ACM}, title = {{Guest editors' introduction to special issue on computational methods in systems biology}}, doi = {10.1145/2745799}, volume = {25}, year = {2015}, } @article{1809, abstract = {Background: Indirect genetic effects (IGEs) occur when genes expressed in one individual alter the expression of traits in social partners. Previous studies focused on the evolutionary consequences and evolutionary dynamics of IGEs, using equilibrium solutions to predict phenotypes in subsequent generations. However, whether or not such steady states may be reached may depend on the dynamics of interactions themselves. Results: In our study, we focus on the dynamics of social interactions and indirect genetic effects and investigate how they modify phenotypes over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics; rather we consider within-individual phenotypic changes, also referred to as phenotypic plasticity. We analyse iterative interactions, when individuals interact in a series of discontinuous events, and investigate the stability of steady state solutions and the dependence on model parameters, such as population size, strength, and the nature of interactions. We show that for interactions where a feedback loop occurs, the possible parameter space of interaction strength is fairly limited, affecting the evolutionary consequences of IGEs. We discuss the implications of our results for current IGE model predictions and their limitations.}, author = {Trubenova, Barbora and Novak, Sebastian and Hager, Reinmar}, journal = {PLoS One}, number = {5}, publisher = {Public Library of Science}, title = {{Indirect genetic effects and the dynamics of social interactions}}, doi = {10.1371/journal.pone.0126907}, volume = {10}, year = {2015}, } @article{1810, abstract = {Combining antibiotics is a promising strategy for increasing treatment efficacy and for controlling resistance evolution. When drugs are combined, their effects on cells may be amplified or weakened, that is the drugs may show synergistic or antagonistic interactions. Recent work revealed the underlying mechanisms of such drug interactions by elucidating the drugs'; joint effects on cell physiology. Moreover, new treatment strategies that use drug combinations to exploit evolutionary tradeoffs were shown to affect the rate of resistance evolution in predictable ways. High throughput studies have further identified drug candidates based on their interactions with established antibiotics and general principles that enable the prediction of drug interactions were suggested. Overall, the conceptual and technical foundation for the rational design of potent drug combinations is rapidly developing.}, author = {Bollenbach, Mark Tobias}, journal = {Current Opinion in Microbiology}, pages = {1 -- 9}, publisher = {Elsevier}, title = {{Antimicrobial interactions: Mechanisms and implications for drug discovery and resistance evolution}}, doi = {10.1016/j.mib.2015.05.008}, volume = {27}, year = {2015}, } @article{1811, abstract = {Atomic form factors are widely used for the characterization of targets and specimens, from crystallography to biology. By using recent mathematical results, here we derive an analytical expression for the atomic form factor within the independent particle model constructed from nonrelativistic screened hydrogenic wave functions. The range of validity of this analytical expression is checked by comparing the analytically obtained form factors with the ones obtained within the Hartee-Fock method. As an example, we apply our analytical expression for the atomic form factor to evaluate the differential cross section for Rayleigh scattering off neutral atoms.}, author = {Safari, Laleh and Santos, José and Amaro, Pedro and Jänkälä, Kari and Fratini, Filippo}, journal = {Journal of Mathematical Physics}, number = {5}, publisher = {American Institute of Physics}, title = {{Analytical evaluation of atomic form factors: Application to Rayleigh scattering}}, doi = {10.1063/1.4921227}, volume = {56}, year = {2015}, } @article{1812, abstract = {We investigate the occurrence of rotons in a quadrupolar Bose–Einstein condensate confined to two dimensions. Depending on the particle density, the ratio of the contact and quadrupole–quadrupole interactions, and the alignment of the quadrupole moments with respect to the confinement plane, the dispersion relation features two or four point-like roton minima or one ring-shaped minimum. We map out the entire parameter space of the roton behavior and identify the instability regions. We propose to observe the exotic rotons by monitoring the characteristic density wave dynamics resulting from a short local perturbation, and discuss the possibilities to detect the predicted effects in state-of-the-art experiments with ultracold homonuclear molecules. }, author = {Lahrz, Martin and Lemeshko, Mikhail and Mathey, Ludwig}, journal = {New Journal of Physics}, number = {4}, publisher = {IOP Publishing}, title = {{Exotic roton excitations in quadrupolar Bose–Einstein condensates }}, doi = {10.1088/1367-2630/17/4/045005}, volume = {17}, year = {2015}, } @article{1813, abstract = {We develop a microscopic theory describing a quantum impurity whose rotational degree of freedom is coupled to a many-particle bath. We approach the problem by introducing the concept of an “angulon”—a quantum rotor dressed by a quantum field—and reveal its quasiparticle properties using a combination of variational and diagrammatic techniques. Our theory predicts renormalization of the impurity rotational structure, such as that observed in experiments with molecules in superfluid helium droplets, in terms of a rotational Lamb shift induced by the many-particle environment. Furthermore, we discover a rich many-body-induced fine structure, emerging in rotational spectra due to a redistribution of angular momentum within the quantum many-body system.}, author = {Schmidt, Richard and Lemeshko, Mikhail}, journal = {Physical Review Letters}, number = {20}, publisher = {American Physical Society}, title = {{Rotation of quantum impurities in the presence of a many-body environment}}, doi = {10.1103/PhysRevLett.114.203001}, volume = {114}, year = {2015}, }